Thought Graph: Generating Thought Process for Biological Reasoning
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arXiv
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| Format: | Preprint |
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2024
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| author | Hsu, Chi-Yang Cox, Kyle Xu, Jiawei Tan, Zhen Zhai, Tianhua Hu, Mengzhou Pratt, Dexter Chen, Tianlong Hu, Ziniu Ding, Ying |
| author_facet | Hsu, Chi-Yang Cox, Kyle Xu, Jiawei Tan, Zhen Zhai, Tianhua Hu, Mengzhou Pratt, Dexter Chen, Tianlong Hu, Ziniu Ding, Ying |
| contents | We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes. Our framework stands out for its ability to provide a deeper understanding of gene sets, significantly surpassing GSEA by 40.28% and LLM baselines by 5.38% based on cosine similarity to human annotations. Our analysis further provides insights into future directions of biological processes naming, and implications for bioinformatics and precision medicine. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_07144 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Thought Graph: Generating Thought Process for Biological Reasoning Hsu, Chi-Yang Cox, Kyle Xu, Jiawei Tan, Zhen Zhai, Tianhua Hu, Mengzhou Pratt, Dexter Chen, Tianlong Hu, Ziniu Ding, Ying Computation and Language We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes. Our framework stands out for its ability to provide a deeper understanding of gene sets, significantly surpassing GSEA by 40.28% and LLM baselines by 5.38% based on cosine similarity to human annotations. Our analysis further provides insights into future directions of biological processes naming, and implications for bioinformatics and precision medicine. |
| title | Thought Graph: Generating Thought Process for Biological Reasoning |
| topic | Computation and Language |
| url | https://arxiv.org/abs/2403.07144 |